Serine proteases are universally found in living organisms, fulfilling a wide variety of functions. In many cases, the serine proteases have specific targets, where precursors are activated to biologically competent products to discharge their particular function. In other cases, there is a more generalized activity, where particular dipeptide sequences within larger proteins are subject to scission in the process of degradation.
Among important serine proteases are trypsin-like enzymes, such as trypsin, tryptase, thrombin, kallikrein, and factor Xa. The serine protease targets are associated with processes such as blood clotting, complement mediated lysis, the immune response, glomerulonephritis, pain sensing, inflammation, pancreatitis, cancer, regulating fertilization, bacterial infection and viral maturation. By inhibiting serine proteases which have high specificity for a particular target, one can inhibit in vivo numerous biological processes, which may have adverse effects on a host.
The serine proteases have a highly conserved active site, where specific amino acids which catalyze the bond scission have a nearly identical spatial arrangement. A complementary binding site adjacent to the active site provides for the primary specificity of the individual serine protease. A succession of indentations or "pockets" along the surface of the protease serve to bind successive side chains along the substrate polypeptide chain on either side of the peptide bond to be cleaved. These are described as P3, P2, P1 prior to the susceptible peptide bond, and P1', P2', P3' after the scissile bond in the substrate, when the peptide sequence is represented in the customary N-to-C terminal manner. Therefore, by providing recognition elements similar to specific amino acid side chains found in the substrate peptide sequences having high affinity to the pockets, one can direct moieties capable of occupying the pocket of the active site to specific serine proteases, so as to restrict the pathways which are inhibited. There is, therefore, substantial interest in identifying inhibitors for the catalytic active site of serine proteases which may be joined to moieties providing specificity for a particular protease.
Relevant Literature
Tidwell et al., J. Med. Chem. (1978) 21:613-623; Geratz et al., Arch. Biochem. Biophys. (1979) 197:551-559; and U.S. Pat. No. 4,940,723 describe bis-(5-amidino-2-benzimidazoylyl)methane and analogs thereof as serine protease inhibitors. Higaki et al., Biochemistry (1990) 29:8582-8586; Kang, Korean J. of Pharmacology (1988) 24:111-123; and Kelly et al., Biochem. J. (1981) 199:129-136 report instances of serine proteases involving the use of zinc.